Mercurial > repos > luis > ball

comparison galaxy_stubs/ProteinCheck.xml @ 2:605370bc1def draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author luis
date Tue, 12 Jul 2016 12:33:33 -0400
parents
children
comparison
equal deleted inserted replaced
1:31013b5cd066 2:605370bc1def
1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
3 <!--Proposed Tool Section: [Checks and evaluations]-->
4 <tool id="ProteinCheck" name="ProteinCheck" version="1.1.0">
5 <description>quality check for proteins structures</description>
6 <macros>
7 <token name="@EXECUTABLE@">ProteinCheck</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="stdio"/>
11 <expand macro="requirements"/>
12 <command>ProteinCheck
13
14 #if $param_i:
15 -i $param_i
16 #end if
17 #if $param_o:
18 -o $param_o
19 #end if
20 #if $param_bc:
21 -bc $param_bc
22 #end if
23 </command>
24 <inputs>
25 <param name="param_i" type="data" format="pdb" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input pdb-file" help="(-i) "/>
26 <param name="param_bc" type="integer" min="0" max="1" optional="True" value="0" label="ignore broken chains" help="(-bc) "/>
27 </inputs>
28 <expand macro="advanced_options"/>
29 <outputs>
30 <data name="param_o" format="pdf"/>
31 </outputs>
32 <help>Check a given protein structure for the following errors:
33 * bond-lengths may not be completely senseless (i.e. &lt;0.7 or &gt;2.5 Angstroem)
34 * each chain may only contain one actual molecule, i.e. there may be no unconnected atoms or fragments. This test is skipped if the above box is checked.
35 * each atom must have a valid assigned element
36 * the protein must be protonated (since this is necessary for docking/(re-)scoring).
37 * 3D coordinates must be present (instead of 2D coordinates; also necessary for docking/(re-)scoring)
38 * there may be no senseless temperature factors (&lt;1 or &gt;100)
39 * there may be no sterical clashes between atoms
40
41 A protein structure quality report, containing the results of those tests and a secondary structure prediction, a Ramachandran plot and a temperature factor plot will be generated and saved as a pdf-file.
42
43 </help>
44 </tool>